niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_dwuncert.py

@@ -0,0 +1,283 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DWUNCERT_METADATA = Metadata(
+    id="8f7f239d86c536d7e540a83e127aed316e05a15c.boutiques",
+    name="3dDWUncert",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDwuncertParameters = typing.TypedDict('V3dDwuncertParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDWUncert"],
+    "input_file": InputPathType,
+    "input_prefix": str,
+    "output_prefix": str,
+    "grad_file": typing.NotRequired[InputPathType | None],
+    "bmatrix_file": typing.NotRequired[InputPathType | None],
+    "num_iters": typing.NotRequired[float | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "calc_thr_fa": typing.NotRequired[float | None],
+    "csf_fa": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dDWUncert": v_3d_dwuncert_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3dDWUncert": v_3d_dwuncert_outputs,
+    }.get(t)
+
+
+class V3dDwuncertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_dwuncert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """AFNI-format file with 6 subbricks, containing uncertainty information."""
+
+
+def v_3d_dwuncert_params(
+    input_file: InputPathType,
+    input_prefix: str,
+    output_prefix: str,
+    grad_file: InputPathType | None = None,
+    bmatrix_file: InputPathType | None = None,
+    num_iters: float | None = None,
+    mask_file: InputPathType | None = None,
+    calc_thr_fa: float | None = None,
+    csf_fa: float | None = None,
+) -> V3dDwuncertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input file with b0 and DWI subbricks.
+        input_prefix: Basename of DTI volumes.
+        output_prefix: Output file name prefix.
+        grad_file: File with 3 columns for x-, y-, and z-comps of DW-gradients.
+        bmatrix_file: File with gradient info in b-matrix format.
+        num_iters: Number of jackknife resample iterations.
+        mask_file: Mask file within which to calculate uncertainty.
+        calc_thr_fa: Threshold for the minimum FA value above which to\
+            calculate uncertainty.
+        csf_fa: Number marking FA value of 'bad' voxels.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDWUncert",
+        "input_file": input_file,
+        "input_prefix": input_prefix,
+        "output_prefix": output_prefix,
+    }
+    if grad_file is not None:
+        params["grad_file"] = grad_file
+    if bmatrix_file is not None:
+        params["bmatrix_file"] = bmatrix_file
+    if num_iters is not None:
+        params["num_iters"] = num_iters
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if calc_thr_fa is not None:
+        params["calc_thr_fa"] = calc_thr_fa
+    if csf_fa is not None:
+        params["csf_fa"] = csf_fa
+    return params
+
+
+def v_3d_dwuncert_cargs(
+    params: V3dDwuncertParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dDWUncert")
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-input",
+        params.get("input_prefix")
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("grad_file") is not None:
+        cargs.extend([
+            "-grads",
+            execution.input_file(params.get("grad_file"))
+        ])
+    if params.get("bmatrix_file") is not None:
+        cargs.extend([
+            "-bmatrix_FULL",
+            execution.input_file(params.get("bmatrix_file"))
+        ])
+    if params.get("num_iters") is not None:
+        cargs.extend([
+            "-iters",
+            str(params.get("num_iters"))
+        ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("calc_thr_fa") is not None:
+        cargs.extend([
+            "-calc_thr_FA",
+            str(params.get("calc_thr_fa"))
+        ])
+    if params.get("csf_fa") is not None:
+        cargs.extend([
+            "-csf_fa",
+            str(params.get("csf_fa"))
+        ])
+    return cargs
+
+
+def v_3d_dwuncert_outputs(
+    params: V3dDwuncertParameters,
+    execution: Execution,
+) -> V3dDwuncertOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dDwuncertOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix") + "+*.HEAD/" + params.get("output_prefix") + "+*.BRIK"),
+    )
+    return ret
+
+
+def v_3d_dwuncert_execute(
+    params: V3dDwuncertParameters,
+    execution: Execution,
+) -> V3dDwuncertOutputs:
+    """
+    Use jackknifing to estimate uncertainty of DTI parameters, important for
+    probabilistic tractography.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDwuncertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_dwuncert_cargs(params, execution)
+    ret = v_3d_dwuncert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_dwuncert(
+    input_file: InputPathType,
+    input_prefix: str,
+    output_prefix: str,
+    grad_file: InputPathType | None = None,
+    bmatrix_file: InputPathType | None = None,
+    num_iters: float | None = None,
+    mask_file: InputPathType | None = None,
+    calc_thr_fa: float | None = None,
+    csf_fa: float | None = None,
+    runner: Runner | None = None,
+) -> V3dDwuncertOutputs:
+    """
+    Use jackknifing to estimate uncertainty of DTI parameters, important for
+    probabilistic tractography.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input file with b0 and DWI subbricks.
+        input_prefix: Basename of DTI volumes.
+        output_prefix: Output file name prefix.
+        grad_file: File with 3 columns for x-, y-, and z-comps of DW-gradients.
+        bmatrix_file: File with gradient info in b-matrix format.
+        num_iters: Number of jackknife resample iterations.
+        mask_file: Mask file within which to calculate uncertainty.
+        calc_thr_fa: Threshold for the minimum FA value above which to\
+            calculate uncertainty.
+        csf_fa: Number marking FA value of 'bad' voxels.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDwuncertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DWUNCERT_METADATA)
+    params = v_3d_dwuncert_params(
+        input_file=input_file,
+        input_prefix=input_prefix,
+        output_prefix=output_prefix,
+        grad_file=grad_file,
+        bmatrix_file=bmatrix_file,
+        num_iters=num_iters,
+        mask_file=mask_file,
+        calc_thr_fa=calc_thr_fa,
+        csf_fa=csf_fa,
+    )
+    return v_3d_dwuncert_execute(params, execution)
+
+
+__all__ = [
+    "V3dDwuncertOutputs",
+    "V3dDwuncertParameters",
+    "V_3D_DWUNCERT_METADATA",
+    "v_3d_dwuncert",
+    "v_3d_dwuncert_params",
+]

niwrap_afni/afni/v_3d_ecm.py

@@ -0,0 +1,363 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ECM_METADATA = Metadata(
+    id="c9bc0ce1e3c30699a348a07653407f3b99801a2a.boutiques",
+    name="3dECM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dEcmParameters = typing.TypedDict('V3dEcmParameters', {
+    "__STYX_TYPE__": typing.Literal["3dECM"],
+    "in_file": InputPathType,
+    "autoclip": bool,
+    "automask": bool,
+    "eps": typing.NotRequired[float | None],
+    "fecm": bool,
+    "full": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "max_iter": typing.NotRequired[int | None],
+    "memory": typing.NotRequired[float | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "polort": typing.NotRequired[int | None],
+    "scale": typing.NotRequired[float | None],
+    "shift": typing.NotRequired[float | None],
+    "sparsity": typing.NotRequired[float | None],
+    "thresh": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dECM": v_3d_ecm_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3dECM": v_3d_ecm_outputs,
+    }.get(t)
+
+
+class V3dEcmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_ecm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output image file name."""
+    out_file_: OutputPathType
+    """Output file."""
+
+
+def v_3d_ecm_params(
+    in_file: InputPathType,
+    autoclip: bool = False,
+    automask: bool = False,
+    eps: float | None = None,
+    fecm: bool = False,
+    full: bool = False,
+    mask: InputPathType | None = None,
+    max_iter: int | None = None,
+    memory: float | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    polort: int | None = None,
+    scale: float | None = None,
+    shift: float | None = None,
+    sparsity: float | None = None,
+    thresh: float | None = None,
+) -> V3dEcmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3decm.
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Mask the dataset to target brain-only voxels.
+        eps: Sets the stopping criterion for the power iteration;\
+            :math:`l2\\|v_\\text{old} - v_\\text{new}\\| < eps\\|v_\\text{old}\\|`;\
+            default = 0.001.
+        fecm: Fast centrality method; substantial speed increase but cannot\
+            accommodate thresholding; automatically selected if -thresh or\
+            -sparsity are not set.
+        full: Full power method; enables thresholding; automatically selected\
+            if -thresh or -sparsity are set.
+        mask: Mask file to mask input data.
+        max_iter: Sets the maximum number of iterations to use in the power\
+            iteration; default = 1000.
+        memory: Limit memory consumption on system by setting the amount of gb\
+            to limit the algorithm to; default = 2gb.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        polort: No description provided.
+        scale: Scale correlation coefficients in similarity matrix to after\
+            shifting, x >= 0.0; default = 1.0 for -full, 0.5 for -fecm.
+        shift: Shift correlation coefficients in similarity matrix to enforce\
+            non-negativity, s >= 0.0; default = 0.0 for -full, 1.0 for -fecm.
+        sparsity: Only take the top percent of connections.
+        thresh: Threshold to exclude connections where corr <= thresh.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dECM",
+        "in_file": in_file,
+        "autoclip": autoclip,
+        "automask": automask,
+        "fecm": fecm,
+        "full": full,
+    }
+    if eps is not None:
+        params["eps"] = eps
+    if mask is not None:
+        params["mask"] = mask
+    if max_iter is not None:
+        params["max_iter"] = max_iter
+    if memory is not None:
+        params["memory"] = memory
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if polort is not None:
+        params["polort"] = polort
+    if scale is not None:
+        params["scale"] = scale
+    if shift is not None:
+        params["shift"] = shift
+    if sparsity is not None:
+        params["sparsity"] = sparsity
+    if thresh is not None:
+        params["thresh"] = thresh
+    return params
+
+
+def v_3d_ecm_cargs(
+    params: V3dEcmParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dECM")
+    cargs.append(execution.input_file(params.get("in_file")))
+    if params.get("autoclip"):
+        cargs.append("-autoclip")
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("eps") is not None:
+        cargs.extend([
+            "-eps",
+            str(params.get("eps"))
+        ])
+    if params.get("fecm"):
+        cargs.append("-fecm")
+    if params.get("full"):
+        cargs.append("-full")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("max_iter") is not None:
+        cargs.extend([
+            "-max_iter",
+            str(params.get("max_iter"))
+        ])
+    if params.get("memory") is not None:
+        cargs.extend([
+            "-memory",
+            str(params.get("memory"))
+        ])
+    cargs.append("[OUT_FILE]")
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "-scale",
+            str(params.get("scale"))
+        ])
+    if params.get("shift") is not None:
+        cargs.extend([
+            "-shift",
+            str(params.get("shift"))
+        ])
+    if params.get("sparsity") is not None:
+        cargs.extend([
+            "-sparsity",
+            str(params.get("sparsity"))
+        ])
+    if params.get("thresh") is not None:
+        cargs.extend([
+            "-thresh",
+            str(params.get("thresh"))
+        ])
+    return cargs
+
+
+def v_3d_ecm_outputs(
+    params: V3dEcmParameters,
+    execution: Execution,
+) -> V3dEcmOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dEcmOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_afni"),
+        out_file_=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3d_ecm_execute(
+    params: V3dEcmParameters,
+    execution: Execution,
+) -> V3dEcmOutputs:
+    """
+    Performs degree centrality on a dataset using a given maskfile via the 3dECM
+    command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dEcmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_ecm_cargs(params, execution)
+    ret = v_3d_ecm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_ecm(
+    in_file: InputPathType,
+    autoclip: bool = False,
+    automask: bool = False,
+    eps: float | None = None,
+    fecm: bool = False,
+    full: bool = False,
+    mask: InputPathType | None = None,
+    max_iter: int | None = None,
+    memory: float | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    polort: int | None = None,
+    scale: float | None = None,
+    shift: float | None = None,
+    sparsity: float | None = None,
+    thresh: float | None = None,
+    runner: Runner | None = None,
+) -> V3dEcmOutputs:
+    """
+    Performs degree centrality on a dataset using a given maskfile via the 3dECM
+    command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3decm.
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Mask the dataset to target brain-only voxels.
+        eps: Sets the stopping criterion for the power iteration;\
+            :math:`l2\\|v_\\text{old} - v_\\text{new}\\| < eps\\|v_\\text{old}\\|`;\
+            default = 0.001.
+        fecm: Fast centrality method; substantial speed increase but cannot\
+            accommodate thresholding; automatically selected if -thresh or\
+            -sparsity are not set.
+        full: Full power method; enables thresholding; automatically selected\
+            if -thresh or -sparsity are set.
+        mask: Mask file to mask input data.
+        max_iter: Sets the maximum number of iterations to use in the power\
+            iteration; default = 1000.
+        memory: Limit memory consumption on system by setting the amount of gb\
+            to limit the algorithm to; default = 2gb.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        polort: No description provided.
+        scale: Scale correlation coefficients in similarity matrix to after\
+            shifting, x >= 0.0; default = 1.0 for -full, 0.5 for -fecm.
+        shift: Shift correlation coefficients in similarity matrix to enforce\
+            non-negativity, s >= 0.0; default = 0.0 for -full, 1.0 for -fecm.
+        sparsity: Only take the top percent of connections.
+        thresh: Threshold to exclude connections where corr <= thresh.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dEcmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ECM_METADATA)
+    params = v_3d_ecm_params(
+        in_file=in_file,
+        autoclip=autoclip,
+        automask=automask,
+        eps=eps,
+        fecm=fecm,
+        full=full,
+        mask=mask,
+        max_iter=max_iter,
+        memory=memory,
+        outputtype=outputtype,
+        polort=polort,
+        scale=scale,
+        shift=shift,
+        sparsity=sparsity,
+        thresh=thresh,
+    )
+    return v_3d_ecm_execute(params, execution)
+
+
+__all__ = [
+    "V3dEcmOutputs",
+    "V3dEcmParameters",
+    "V_3D_ECM_METADATA",
+    "v_3d_ecm",
+    "v_3d_ecm_params",
+]